MolNFT v1 · #156769 · protein

PCDHGB3 EC1-4 in 50 mm hepes

6MER · Protocadherin gamma-B3: “PCDHGB3 EC1-4 in 50 mm hepes”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.35). MolNFT v1 #156769 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6MER
Type: protein
Length: 414 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protocadherin gamma-B3
UniProt: Q9Y5G1
Ligands: CA
Pockets: 2 · best druggability 0.35

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protocadherin gamma-B3	protein	414	6% helix, 45% strand	Q9Y5G1

Ligands and binding sites

CA · Calcium ion · metal · 9 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	52	0.35	0.79	12	empty
2	55	0.27	0.74	18	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6MER · PcdhgB3 EC1-4 in 50 mM HEPES · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y5G1 · AlphaFold monomer V2.0 prediction for protocadherin gamma-B3 (Q9Y5G1) · a predicted model of the same protein · chain A against A, TM-score 0.92

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9Y5G1
Elsewhere: RCSB PDB 6MER · PDBe 6MER · UniProt Q9Y5G1

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